agreed- this was the conversation we had started during the meeting,
just wanted Jason to know that we had been discussing it since he
wasn't there.
carlos
On Fri, Apr 8, 2011 at 12:02 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Carlos,
>
>> we should keep this discussion going- I think you missed out on the
>> HREMD brainstorming session at the bar during the amber meeting.
>> exchanging coordinates will likely be quite inefficient for many
>> problems, but needed for others. we talked a lot about how we need to
>> generalize the exchange, and really track down impact on the code (for
>> example, needing to redo load balancing and spatial decomposition
>> work, etc).
>
> Indeed exchanging coordinates is VERY general but inefficient which is why
> we implemented the Temperature REMD first to get the framework in place but
> avoid having coordinate exchanges. Obviously we need to do this slowly to be
> careful of breaking existing performance in PMEMD and other things as well
> such as the REMD changes that went in breaking the GPU code etc. But things
> are looking good and Jason's numbers so far for just Temperature REMD look
> awesome from a performance perspective. The next step is to implement a
> general REMD method but I think we (you, me, Jason and Adrian) should talk
> about this offline to determine the optimum way of doing this. Exchanging
> coordinates is general but is not going to cut it at all from a performance
> perspective, unless you limit exchanges to every 1000 steps or so.
>
> I think one thing we need is an exact definition of what information is
> needed for which type of exchange. This needs to be detailed and represent
> the minimum amount of information that would need to be exchanged. For
> example just saying exchange coordinates is easy but really doesn't help
> solve the problem. So if someone wants to volunteer to document specifically
> which type of exchanges should be supported and what the specifications for
> each type of exchange are, along with working out the minimum information we
> can get away with exchanging that would be very helpful.
>
> Probably best we discuss this between a few of us over skype to avoid lots
> of confusion, although having a side discussion on here is probably useful
> as well.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Fri Apr 08 2011 - 09:30:06 PDT
